RegulonDB RegulonDB 10.10: Gene Form
   

cydA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mngB cydA cydB ArcA Cra Cra ArcA FNR FNR ArcA ArcA ArcA ArcA ybgEp4 ybgEp4 TSS_888 TSS_888 TSS_887 TSS_887 TSS_886 TSS_886 TSS_885 TSS_885 TSS_884 (cluster) TSS_884 (cluster) TSS_883 TSS_883 TSS_882 TSS_882 TSS_881 TSS_881 TSS_880 TSS_880 TSS_879 TSS_879 TSS_878 TSS_878 TSS_877 TSS_877 TSS_876 TSS_876 TSS_875 TSS_875 TSS_874 TSS_874 TSS_873 TSS_873 TSS_872 TSS_872 TSS_871 TSS_871 TSS_870 TSS_870 TSS_869 TSS_869 TSS_868 TSS_868 TSS_867 TSS_867 TSS_866 TSS_866 TSS_865 TSS_865 cydAp5 cydAp5 TSS_864 TSS_864 cydAp2 cydAp2 TSS_862 TSS_862 cydAp4 cydAp4 cydAp3 cydAp3 cydAp1 cydAp1

Gene      
Name: cydA    Texpresso search in the literature
Synonym(s): ECK0721, EG10173, b0733, cyd-1
Genome position(nucleotides): 771458 --> 773026 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.9
External database links:  
ASAP:
 ABE-0002499
CGSC:
 10369
ECHOBASE:
 EB0170
ECOLIHUB:
 cydA
OU-MICROARRAY:
 b0733
STRING:
 511145.b0733
COLOMBOS: cydA


Product      
Name: cytochrome bd-I ubiquinol oxidase subunit I
Synonym(s): Cyd-1, CydA
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 58.205
Isoelectric point: 6.795
Motif(s):
 
Type Positions Sequence
15 -> 34 TAMYHFLFVPLTLGMAFLLA
126 -> 126 H
187 -> 203 TVASGYVTGAMFILGIS
213 -> 213 F
447 -> 451 GRQPW

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
GO:0070069 - cytochrome complex
molecular_function GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0046872 - metal ion binding
GO:0016679 - oxidoreductase activity, acting on diphenols and related substances as donors
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0020037 - heme binding
biological_process GO:0006119 - oxidative phosphorylation
GO:0019646 - aerobic electron transport chain
Note(s): Note(s): ...[more].
Reference(s): [1] Belevich I., et al., 2005
[2] Borisov VB., et al., 2008
[3] Chorev DS., et al., 2018
[4] Goojani HG., et al., 2020
[5] Mogi T. 2009
[6] Newton G., et al., 1991
[7] Ovchinnikov S., et al., 2015
[8] Zhang J., et al., 2004
External database links:  
DIP:
 DIP-36181N
ECOCYC:
 CYDA-MONOMER
ECOLIWIKI:
 b0733
ECOO157CYC:
 CYDA-MONOMER
INTERPRO:
 IPR002585
MINT:
 P0ABJ9
PANTHER:
 PTHR30365
PDB:
 6RKO
PDB:
 6RX4
PFAM:
 PF01654
PRIDE:
 P0ABJ9
PRODB:
 PRO_000022361
REFSEQ:
 NP_415261
SMR:
 P0ABJ9
UNIPROT:
 P0ABJ9


Operon      
Name: cydAB         
Operon arrangement:
Transcription unit        Promoter
cydAB
cydAB
cydAB
cydAB
cydAB


Transcriptional Regulation      
Display Regulation             
Activated by: FNR, Cra, ArcA, HypT
Repressed by: H-NS, FNR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_862 771280 forward nd [RS-EPT-CBR] [9]
  promoter TSS_864 771302 forward nd [RS-EPT-CBR] [9]
  promoter TSS_865 771369 forward nd [RS-EPT-CBR] [9]
  promoter TSS_866 771383 forward nd [RS-EPT-CBR] [9]
  promoter TSS_867 771385 forward nd [RS-EPT-CBR] [9]
  promoter TSS_868 771778 forward nd [RS-EPT-CBR] [9]
  promoter TSS_869 771784 forward nd [RS-EPT-CBR] [9]
  promoter TSS_870 771797 forward nd [RS-EPT-CBR] [9]
  promoter TSS_871 771799 forward nd [RS-EPT-CBR] [9]
  promoter TSS_872 771802 forward nd [RS-EPT-CBR] [9]
  promoter TSS_873 771808 forward nd [RS-EPT-CBR] [9]
  promoter TSS_874 772115 forward nd [RS-EPT-CBR] [9]
  promoter TSS_875 772368 forward nd [RS-EPT-CBR] [9]
  promoter TSS_876 772487 forward nd [RS-EPT-CBR] [9]
  promoter TSS_877 773190 forward nd [RS-EPT-CBR] [9]
  promoter TSS_878 773198 forward nd [RS-EPT-CBR] [9]
  promoter TSS_879 773312 forward nd [RS-EPT-CBR] [9]
  promoter TSS_880 773782 forward nd [RS-EPT-CBR] [9]
  promoter TSS_881 773787 forward nd [RS-EPT-CBR] [9]
  promoter TSS_882 773945 forward nd [RS-EPT-CBR] [9]
  promoter TSS_883 773948 forward nd [RS-EPT-CBR] [9]
  promoter TSS_884 (cluster) 773972 forward nd [RS-EPT-CBR] [9]
  promoter TSS_885 774006 forward nd [RS-EPT-CBR] [9]
  promoter TSS_886 774011 forward nd [RS-EPT-CBR] [9]
  promoter TSS_887 774017 forward nd [RS-EPT-CBR] [9]
  promoter TSS_888 774033 forward nd [RS-EPT-CBR] [9]
  promoter ybgEp4 774150 forward nd [ICWHO] [10]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Belevich I., Borisov VB., Zhang J., Yang K., Konstantinov AA., Gennis RB., Verkhovsky MI., 2005, Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site., Proc Natl Acad Sci U S A 102(10):3657-62

 [2] Borisov VB., Belevich I., Bloch DA., Mogi T., Verkhovsky MI., 2008, Glutamate 107 in subunit I of cytochrome bd from Escherichia coli is part of a transmembrane intraprotein pathway conducting protons from the cytoplasm to the heme b595/heme d active site., Biochemistry 47(30):7907-14

 [3] Chorev DS., Baker LA., Wu D., Beilsten-Edmands V., Rouse SL., Zeev-Ben-Mordehai T., Jiko C., Samsudin F., Gerle C., Khalid S., Stewart AG., Matthews SJ., Grunewald K., Robinson CV., 2018, Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry., Science 362(6416):829-834

 [4] Goojani HG., Konings J., Hakvoort H., Hong S., Gennis RB., Sakamoto J., Lill H., Bald D., 2020, The carboxy-terminal insert in the Q-loop is needed for functionality of Escherichia coli cytochrome bd-I., Biochim Biophys Acta Bioenerg 1861(5-6):148175

 [5] Mogi T., 2009, Probing the haem d-binding site in cytochrome bd quinol oxidase by site-directed mutagenesis., J Biochem 145(6):763-70

 [6] Newton G., Gennis RB., 1991, In vivo assembly of the cytochrome d terminal oxidase complex of Escherichia coli from genes encoding the two subunits expressed on separate plasmids., Biochim Biophys Acta 1089(1):8-12

 [7] Ovchinnikov S., Kinch L., Park H., Liao Y., Pei J., Kim DE., Kamisetty H., Grishin NV., Baker D., 2015, Large-scale determination of previously unsolved protein structures using evolutionary information., Elife 4:e09248

 [8] Zhang J., Hellwig P., Osborne JP., Gennis RB., 2004, Arginine 391 in subunit I of the cytochrome bd quinol oxidase from Escherichia coli stabilizes the reduced form of the hemes and is essential for quinol oxidase activity., J Biol Chem 279(52):53980-7

 [9] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [10] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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